[cctbxbb] bootstrap.py build on Ubuntu

Billy Poon bkpoon at lbl.gov
Tue Jun 14 13:44:42 PDT 2016 

Hi David,

Scratch the lib64z1 and lib64z1-dev packages. Apparently, those are for
i386.

For 12.04, 14.04, and 16.04, libz.so is placed in /usr/lib/x86_64-linux-gnu
by the zlib1g-dev package. It looks like Ubuntu libraries are now placed in
a directory named by architecture to better support multiple architectures
on the same machine.

I updated install_base_packages to supply that directory for building PIL.
This is specific to x86_64, so this won't work on 32-bit Ubuntu. But if you
want a 32-bit Ubuntu build, installing lib64z1-dev should work.

Let me know if you have any more issues. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org

On Tue, Jun 14, 2016 at 11:29 AM, David Waterman <dgwaterman at gmail.com>
wrote:

> Hey Billy,
>
> Thanks. I'm travelling at the moment, but once I'm back I'll give that a
> go.
>
> Cheers
> David
>
> On Tue, 14 Jun 2016, 17:34 Billy Poon, <bkpoon at lbl.gov> wrote:
>
>> Hi David,
>>
>> Actually, it looks like the lib64z1-dev package provides libz.so in
>> /usr/lib64, so installing that package should fix your issue. It's a bit
>> odd that the lib64z1 package does not provide that file.
>>
>> --
>> Billy K. Poon
>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> 1 Cyclotron Road, M/S 33R0345
>> Berkeley, CA 94720
>> Tel: (510) 486-5709
>> Fax: (510) 486-5909
>> Web: https://phenix-online.org
>>
>> On Mon, Jun 13, 2016 at 1:53 PM, Billy Poon <bkpoon at lbl.gov> wrote:
>>
>>> Hi David,
>>>
>>> I don't have a fix yet, but here is a workaround. It seems like setup.py
>>> is looking for libz.so instead of libz.so.1, so you can fix the issue by
>>> making a symbolic link for libz.so in /usr/lib64.
>>>
>>> sudo ln -s /usr/lib64/libz.so.1 /usr/lib64/libz.so
>>>
>>> This requires root access, so that's why it's just a workaround.
>>>
>>> --
>>> Billy K. Poon
>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> 1 Cyclotron Road, M/S 33R0345
>>> Berkeley, CA 94720
>>> Tel: (510) 486-5709
>>> Fax: (510) 486-5909
>>> Web: https://phenix-online.org
>>>
>>> On Sat, Jun 11, 2016 at 5:05 PM, Billy Poon <bkpoon at lbl.gov> wrote:
>>>
>>>> Hi David,
>>>>
>>>> Sorry it look so long! Setting up all the virtual machines was a time
>>>> sink and getting things to work on 32-bit CentOS 5 and Ubuntu 12.04 was a
>>>> little tricky.
>>>>
>>>> It looks like Ubuntu 16.04 moved its libraries around. I used apt-get
>>>> to install libz-dev and lib64z1 (the 64-bit library). There is a libz.so.1
>>>> file in /lib/x86_64-linux-gnu and in /usr/lib64.
>>>>
>>>> I have not gotten it to work yet, but I'm pretty sure this is the
>>>> issue. I'll have to double-check 12.04 and 14.04.
>>>>
>>>> As for Pillow, I did test it a few months ago, but I remember there
>>>> being API changes that will need to fixed.
>>>>
>>>> --
>>>> Billy K. Poon
>>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>>>> Lawrence Berkeley National Laboratory
>>>> 1 Cyclotron Road, M/S 33R0345
>>>> Berkeley, CA 94720
>>>> Tel: (510) 486-5709
>>>> Fax: (510) 486-5909
>>>> Web: https://phenix-online.org
>>>>
>>>> On Sat, Jun 11, 2016 at 2:04 AM, David Waterman <dgwaterman at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Billy,
>>>>>
>>>>> I'm replying on this old thread because I have finally got round to
>>>>> trying a bootstrap build for DIALS out again on Ubuntu, having waited for
>>>>> updates to the dependencies and updating the OS to 16.04.
>>>>>
>>>>> The good news is, the build ran through fine. This is the first time
>>>>> I've had a bootstrap build complete without error on Ubuntu, so thanks to
>>>>> you and the others who have worked on improving the build in the last few
>>>>> months!
>>>>>
>>>>> The bad news is I'm getting two failures in the DIALS tests:
>>>>>
>>>>> dials/test/command_line/tst_export_bitmaps.py
>>>>> dials_regression/test.py
>>>>>
>>>>> Both are from PIL
>>>>>
>>>>>       File
>>>>> "/home/fcx32934/dials_test_build/base/lib/python2.7/site-packages/PIL/Image.py",
>>>>> line 401, in _getencoder
>>>>>         raise IOError("encoder %s not available" % encoder_name)
>>>>>     IOError: encoder zip not available
>>>>>
>>>>> Indeed, from base_tmp/imaging_install_log it looks like PIL is not
>>>>> configured properly
>>>>>
>>>>> --------------------------------------------------------------------
>>>>> PIL 1.1.7 SETUP SUMMARY
>>>>> --------------------------------------------------------------------
>>>>> version       1.1.7
>>>>> platform      linux2 2.7.8 (default_cci, Jun 10 2016, 16:04:32)
>>>>>               [GCC 5.3.1 20160413]
>>>>> --------------------------------------------------------------------
>>>>> *** TKINTER support not available
>>>>> *** JPEG support not available
>>>>> *** ZLIB (PNG/ZIP) support not available
>>>>> *** FREETYPE2 support not available
>>>>> *** LITTLECMS support not available
>>>>> --------------------------------------------------------------------
>>>>>
>>>>> Any ideas? I have zlib headers but perhaps PIL can't find them.
>>>>>
>>>>> On a related note, the free version of PIL has not been updated for
>>>>> years. The replacement Pillow has started to diverge. I first noticed this
>>>>> when Ubuntu 16.04 gave me Pillow 3.1.2 and my cctbx build with the system
>>>>> python produced failures because it no longer supports certain deprecated
>>>>> methods from PIL. I worked around that in r24587, but these things are a
>>>>> losing battle. Is it time to switch cctbx over to Pillow instead of PIL?
>>>>>
>>>>> Cheers
>>>>>
>>>>> -- David
>>>>>
>>>>> On 7 January 2016 at 18:12, Billy Poon <bkpoon at lbl.gov> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> Since wxPython was updated to 3.0.2, I have been thinking about
>>>>>> updating the other GUI-related packages to more recent versions. I would
>>>>>> probably update to the latest, stable version that does not involve major
>>>>>> changes to the API so that backwards compatibility is preserved. Let me
>>>>>> know if that would be helpful and I can prioritize the migration and
>>>>>> testing.
>>>>>>
>>>>>> --
>>>>>> Billy K. Poon
>>>>>> Research Scientist, Molecular Biophysics and Integrated Bioimaging
>>>>>> Lawrence Berkeley National Laboratory
>>>>>> 1 Cyclotron Road, M/S 33R0345
>>>>>> Berkeley, CA 94720
>>>>>> Tel: (510) 486-5709
>>>>>> Fax: (510) 486-5909
>>>>>> Web: https://phenix-online.org
>>>>>>
>>>>>> On Thu, Jan 7, 2016 at 9:30 AM, Nicholas Sauter <nksauter at lbl.gov>
>>>>>> wrote:
>>>>>>
>>>>>>> David,
>>>>>>>
>>>>>>> I notice that the Pango version, 1.16.1, was released in 2007, so
>>>>>>> perhaps it is no surprise that the latest Ubuntu does not support it.
>>>>>>> Maybe this calls for stepping forward the Pango version until you find one
>>>>>>> that works. I see that the latest stable release is 1.39.
>>>>>>>
>>>>>>> This would be valuable information for us..Billy Poon in the Phenix
>>>>>>> group is supporting the Phenix GUI, so it might be advisable for him to
>>>>>>> update the Pango version in the base installer.
>>>>>>>
>>>>>>> Nick
>>>>>>>
>>>>>>> Nicholas K. Sauter, Ph. D.
>>>>>>> Computer Staff Scientist, Molecular Biophysics and Integrated
>>>>>>> Bioimaging Division
>>>>>>> Lawrence Berkeley National Laboratory
>>>>>>> 1 Cyclotron Rd., Bldg. 33R0345
>>>>>>> Berkeley, CA 94720
>>>>>>> (510) 486-5713
>>>>>>>
>>>>>>> On Thu, Jan 7, 2016 at 8:54 AM, David Waterman <dgwaterman at gmail.com
>>>>>>> > wrote:
>>>>>>>
>>>>>>>> Hi again
>>>>>>>>
>>>>>>>> Another data point: I just tried this on a different Ubuntu
>>>>>>>> machine, this time running 14.04. In this case pango installed just fine.
>>>>>>>> In fact all other packages installed too and the machine is now compiling
>>>>>>>> cctbx.
>>>>>>>>
>>>>>>>> I might have enough for comparison between the potentially working
>>>>>>>> 14.04 and failed 15.04 builds to figure out what is wrong in the second
>>>>>>>> case.
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>>
>>>>>>>> -- David
>>>>>>>>
>>>>>>>> On 7 January 2016 at 09:56, David Waterman <dgwaterman at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi folks
>>>>>>>>>
>>>>>>>>> I recently tried building cctbx+dials on Ubuntu 15.04 following
>>>>>>>>> the instructions here:
>>>>>>>>> http://dials.github.io/documentation/installation_developer.html
>>>>>>>>>
>>>>>>>>> This failed during installation of pango-1.16.1. Looking
>>>>>>>>> at pango_install_log, I see the command that failed was as follows:
>>>>>>>>>
>>>>>>>>> gcc -DHAVE_CONFIG_H -I. -I. -I../..
>>>>>>>>> -DSYSCONFDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/etc\"
>>>>>>>>> -DLIBDIR=\"/home/fcx32934/sw/dials_bootstrap_test/base/lib\"
>>>>>>>>> -DG_DISABLE_CAST_CHECKS -I../.. -DG_DISABLE_DEPRECATED
>>>>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include
>>>>>>>>> -I/home/fcx32934/sw/dials_bootstrap_test/base/include/freetype2 -g -O2
>>>>>>>>> -Wall -MT fribidi.lo -MD -MP -MF .deps/fribidi.Tpo -c fribidi.c  -fPIC
>>>>>>>>> -DPIC -o .libs/fribidi.o
>>>>>>>>> In file included from fribidi.h:31:0,
>>>>>>>>>                  from fribidi.c:28:
>>>>>>>>> fribidi_config.h:1:18: fatal error: glib.h: No such file or
>>>>>>>>> directory
>>>>>>>>>
>>>>>>>>> The file glib.h appears to be in base/include/glib-2.0/, however
>>>>>>>>> this directory was not explicitly included in the command above, only its
>>>>>>>>> parent. This suggests a configuration failure in pango to me. Taking a look
>>>>>>>>> at base_tmp/pango-1.16.1/config.log, I see what look like the relevant
>>>>>>>>> lines:
>>>>>>>>>
>>>>>>>>> configure:22227: checking for GLIB
>>>>>>>>> configure:22235: $PKG_CONFIG --exists --print-errors
>>>>>>>>> "$GLIB_MODULES"
>>>>>>>>> configure:22238: $? = 0
>>>>>>>>> configure:22253: $PKG_CONFIG --exists --print-errors
>>>>>>>>> "$GLIB_MODULES"
>>>>>>>>> configure:22256: $? = 0
>>>>>>>>> configure:22304: result: yes
>>>>>>>>>
>>>>>>>>> but this doesn't tell me very much. Does anyone have any
>>>>>>>>> suggestions as to how I might proceed?
>>>>>>>>>
>>>>>>>>> Many thanks
>>>>>>>>>
>>>>>>>>> -- David
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> cctbxbb mailing list
>>>>>>>> cctbxbb at phenix-online.org
>>>>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>>>>
>>>>>>>>
>>>>>>>
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>>>>>>>
>>>>>>>
>>>>>>
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>>>>>>
>>>>>
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